[gmx-users] HELP REGARDING COMMAND g_pvd

Hello all, I saw a command in the analysis part of manual in section 8.14 . The command name is g_pvd . It says it can calculate properties like density of particles per unit volume but I donot find it in the manual nor in my GROMACS installation. Can anybody help me on this? Avinash Kumar

Re: [gmx-users] Gel Phase in DMPC using Berger force field ??

Sorry. I simulate DOPG not POPG. Thank you anyway. On Dec 13, 2007 6:53 PM, Alan Dodd <[EMAIL PROTECTED]> wrote: > What topology are you using? If you're using one based on the Kartunnen's > group POPG (the only publicly available one I know of), then be aware that I > think they saw gel phas

Re: [gmx-users] How to choose lipid molecules?

liang wrote: > Dear Jochen, > > Thanks for your information. Can you provide me some references about > lipid types and properties, > and the combimation of the recent "popular" membrance proteins (KcsA, > OmpA, M2, Gramacidin A and Aquaporin) ? > I have searched several publications, but still did

Re: [gmx-users] Reproducing runs

Ranjani Krishnan wrote: Hi, I have noticed that I cannot reproduce MD runs exactly -- running the exact same .tpr file again gives different results. From previous posts, I have seen some explanations for this. However, if I do AFM pulling simulations, I am able to reproduce them exactly –

RE: [gmx-users] problem with npt

thanks for your help. My system ran fine for 250 ps but later the bilayer deformed very much. my mdp is integrator = md dt = 0.002; ps ! nsteps = 125000 ; total 100 ps. nstcomm = 1 nstxout = 250 nstenergy = 100 n

Re: [gmx-users] problem with npt

pragya chohan wrote: thanks for your help. My system ran fine for 250 ps but later the bilayer deformed very much. What was your system preparation protocol - i.e. minimization and equilibration? See http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation Mark _

[gmx-users] g_potential problem

Hello! I am a new beginner of Gromacs. I am trying to use g_potential to calculate the potential across the membrane. But I only got the 2D plot (potential vs x axis). Can I get the 3D plot (potential vs x vs y) by using g_potential? Thanks in advance for your kind help! Candy

[gmx-users] Warning message with 3.3.2 but not 3.3.1

Hi, I am running AFM pulling simulations on an integrin-RGD system. I have tried running the exact same simulation in version 3.3.1 and version 3.3.2, and I am getting a large VCM message in 3.3.2, but not 3.3.1. Here are the cases that I have tried: 1) Version 3.2.1: The integrin rec

[gmx-users] Reproducing runs

Hi, I have noticed that I cannot reproduce MD runs exactly -- running the exact same .tpr file again gives different results. From previous posts, I have seen some explanations for this. However, if I do AFM pulling simulations, I am able to reproduce them exactly - running the same simulation

[gmx-users] rtp

Hi! I am attempting to simulate a protein with a modified amino acid using the Gromacs force field with hydrogens for NMR. I have built the RTP and TOP files using PRODRG. I need to know what is the rtp file? relevant to the above force field such that I can append my rtp file. Is it the ffgmx2

Re: [gmx-users] rtp

Dear Jayant, I might be wrong, but I think the original gmx force field that you are referring to has been deprecated. Best wishes, Art On Dec 14, 2007, at 1:44 PM, jayant_jacques wrote: Hi! I am attempting to simulate a protein with a modified amino acid using the Gromacs force field wi

Re: [gmx-users] rtp

jayant_jacques wrote: Hi! I am attempting to simulate a protein with a modified amino acid using the Gromacs force field with hydrogens for NMR. I have built the RTP and TOP files using PRODRG. I need to know what is the rtp file? relevant to the above force field such that I can append my rtp